RetrogeneDB ID: retro_cjac_3482

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01181484.1:11309..12111(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015967
• Aliases: None
• Description: None

Sequence

>retro_cjac_3482
TCATCCCACTGCCATGTGACCCTCAGTTCCTCAGAGACAGTGAGTGAGCTCAACTCTCAGGCTATCATTCACACTCAGCG
TGAAAAGGCAGCAGATTCACTACCAAGGGAGAAACTGGCCCCCAGGAATGGCTCCCCAACATCTCAAAAGTCTAGGCCTC
GTAGAAAGAAATATCCTCCGCTGCCATGCAGCGAAGGGGAGCCTCTGATGCTGCCCCCTCCCTTACAGCTGGGGTTCCAG
ATCACTGCTGAAGACCTGGACCTGGAGAAGGAGGCGACGCTCCGGGGCATTAATAGTGCACTTCGGGGTGAGGTCAAGGC
CATCTGGGACTGTAGAGCCTCACAGCCTTCACAAGCTTTGTCCTCACCTGCAACAGGGACTACTTGTCTGCCTGCTGTCC
CTGAAGCACCCAGCATGGATGCACATCAGCAGACTCACAAGTCCCAACAGTACCTGGACCACCTGTCCCTCCTAGCATCT
GCTGCAGGGGACCCCTCTAGACCTGCTGTGTCTGGGAGGAAGCACCGCTCATCAGGCCCCCTGTTCTCCTAAGAGCCCCT
TCCTGACACCACTTCACACTCCCGGGACACAGCCCAGGTCACCTCCCTGATTCCTGCCCCCTTCCCAGCTCCACGTGCGG
ACTGCAGCCTGAGAAGCGCAAGGCCTGGCACTTCTGCTGCTGCAGCTGCCGCAGGGGCCCTTACCCCCTCTACATGGAAC
CCTTCATGGGGGGCCCCACCGAGTGGAGGGCAAAGAGGCCCCTCACATCCCTGGGCCTCAGCCACAGCTGCAGCAGGTGC
CC

Alignment

ORF - retro_cjac_3482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 66.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSHCHVTLSSSKTVSEDNSQAVSQAVIHTQGEKAADAPPGEKLAPRNGSPTYQESRPCRRKFPLLPRRQR
          SSHCHVTLSSS.TVSE.N....SQA.IHTQ.EKAAD..P.EKLAPRNGSPT.Q.SRP.R.K.P.LP....
Retrocopy SSHCHVTLSSSETVSELN----SQAIIHTQREKAADSLPREKLAPRNGSPTSQKSRPRRKKYPPLPCSEG

Parental  EPLMLPPPLQLGYRVTAEDMDLEKEAGIQCINSALQGEVKAIRDCRASQPSQALSSPATGSS-PPAVPKV
          EPLMLPPPLQLG...TAED.DLEKEA....INSAL.GEVKAI.DCRASQPSQALSSPATG....PAVP..
Retrocopy EPLMLPPPLQLGFQITAEDLDLEKEATLRGINSALRGEVKAIWDCRASQPSQALSSPATGTTCLPAVPEA

Parental  PSMDAHQQTHKSQQYLGHLSLLASAAGDPSRPAVSGRKRRSSGPLFSYSYPLPDTPSHPRDTAQVTSLIP
          PSMDAHQQTHKSQQYL.HLSLLASAAGDPSRPAVSGRK.RSSGPLFS...PLPDT.SH.RDTAQVTSLIP
Retrocopy PSMDAHQQTHKSQQYLDHLSLLASAAGDPSRPAVSGRKHRSSGPLFS*E-PLPDTTSHSRDTAQVTSLIP

Parental  APFPAPRADCSLRSPRPGTSAAAAAAGALTPSTWNPSWGS-HRVEGKEAPHIPGPQPQLQQVP
          APFPAPRADCSLRS.RPGTSAAAAAAGALTPSTWNPSWG..HRVEGKEAPHIPGPQPQLQQVP
Retrocopy APFPAPRADCSLRSARPGTSAAAAAAGALTPSTWNPSWGA>HRVEGKEAPHIPGPQPQLQQVP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.02 RPM	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.02 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3482 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3482 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002950	1 retrocopy	retro_cjac_1098,
Callithrix jacchus	ENSCJAG00000015967	2 retrocopies	retro_cjac_3482 , retro_cjac_645,